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- PDB-6g61: Crystal structure of thioredoxin O1 from Arabidopsis thaliana in ... -

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Basic information

Entry
Database: PDB / ID: 6g61
TitleCrystal structure of thioredoxin O1 from Arabidopsis thaliana in oxidized state
ComponentsThioredoxin O1, mitochondrial
KeywordsOXIDOREDUCTASE / Thioredoxin
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / mitochondrial matrix / endoplasmic reticulum / mitochondrion / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin O1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsRoret, T. / Didierjean, C.
CitationJournal: Antioxidants (Basel) / Year: 2018
Title: MitochondrialArabidopsis thalianaTRXo Isoforms Bind an Iron−Sulfur Cluster and Reduce NFU Proteins In Vitro.
Authors: Zannini, F. / Roret, T. / Przybyla-Toscano, J. / Dhalleine, T. / Rouhier, N. / Couturier, J.
History
DepositionMar 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin O1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)14,5951
Polymers14,5951
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.151, 39.242, 79.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thioredoxin O1, mitochondrial / AtTrxo1


Mass: 14594.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g35010, F19I3.24 / Production host: Escherichia coli (E. coli) / References: UniProt: O64764
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.92 %
Crystal growTemperature: 277 K / Method: microbatch / Details: 100 mM HEPES buffer (pH 7.5) 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9799 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9799 Å / Relative weight: 1
ReflectionResolution: 1.8→39.67 Å / Num. obs: 11316 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.049 / Rrim(I) all: 0.131 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 7 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 7 / Num. unique obs: 653 / CC1/2: 0.961 / Rpim(I) all: 0.145 / Rrim(I) all: 0.283 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2722: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
MolProbitymodel building
RefinementResolution: 1.8→39.67 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.48
RfactorNum. reflection% reflection
Rfree0.2396 524 4.66 %
Rwork0.2196 --
obs0.2207 11236 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 0 130 985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002873
X-RAY DIFFRACTIONf_angle_d0.4741182
X-RAY DIFFRACTIONf_dihedral_angle_d12.079526
X-RAY DIFFRACTIONf_chiral_restr0.044136
X-RAY DIFFRACTIONf_plane_restr0.003149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.98120.30991090.2962620X-RAY DIFFRACTION99
1.9812-2.26790.32641240.24762650X-RAY DIFFRACTION100
2.2679-2.85720.27191290.23412672X-RAY DIFFRACTION100
2.8572-39.67940.19191620.18852770X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.89361.3984-2.18091.2515-1.31864.74540.0477-0.3992-0.36980.2772-0.3317-0.10340.22790.6781-0.59730.2701-0.02630.01460.20850.02850.2174.777-7.233-10.1255
20.1860.10.57071.08611.18282.80320.0737-0.1560.03250.2488-0.20110.10910.0525-0.344-0.45230.201-0.0412-0.01680.19610.00130.10861.66540.9597-9.2202
30.5103-0.76120.18531.1468-0.24660.1453-0.1574-0.2217-0.18080.22620.14570.392-0.0052-0.18270.0150.215-0.00220.04170.2563-0.00330.1816-7.13620.5926-5.7722
40.59060.3277-0.56681.7494-0.06480.58490.059-0.12820.11070.3477-0.16290.15740.12140.34-0.14430.37520.0759-0.12440.3095-0.10530.262610.3405-0.73780.1199
50.0303-0.0765-0.01030.19330.0260.0035-0.00870.09040.00330.040.0516-0.0748-0.00010.07240.14080.4745-0.1957-0.22250.84620.18290.498413.6677-0.1064-6.2172
60.3903-0.56560.10691.20680.22292.2895-0.4422-0.12510.0019-0.18850.1621-0.2375-0.60140.5086-0.22490.36290.00080.01560.3001-0.02490.20599.33628.0715-7.4746
70.1556-0.31790.25920.7794-0.55440.43630.02380.04280.06860.1531-0.08020.2053-0.1729-0.11930.00120.2068-0.01760.00370.2077-0.01540.1577-4.6516.8064-15.0136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 63 )
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 73 )
6X-RAY DIFFRACTION6chain 'A' and (resid 74 through 82 )
7X-RAY DIFFRACTION7chain 'A' and (resid 83 through 113 )

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